transmart/transmart-data — pull request #51 by evast (2014-12-19 13:37:32+00:00)
Title: Import XNAT (image derived) clinical data in TranSMART (transmartApp)

Dear TranSMART developers,

This is a joined pull request for the following projects, as changes to both projects are required to work correctly:

transmartApp
transmart-data
The code in this pull request implements functionality to import XNAT (image derived) clinical data (numerical, text) to TranSMART. The purpose is to make it possible to correlate image derived data with other clinical data in TranSMART.

Summary of functionality: A new group is added to the admin panel, with several new webpages to configure the coupling. I think the admin panel is the best place for this, as TranSMART is a dataware house where an admin imports the data, and currently the normal user cannot import data by themself. The coupling configuration in the admin panels configures which XNAT atribute (via REST api call) is linked to which node in TranSMART. Several configurations can be created for multiple projects and re-used for data updates later. An administrator can create such a configuration once, save it for later, and import the XNAT data. The data is imported (under the hood) by a python script in transmart-data to a local mapping and data file (.tmm and .tmd). Then the default Kettle job for clinical data imports the XNAT data. The data is then visible in TranSMART in the dataset explorer. Note that no ssh access to the server is required to import the data, the python and Kettle scripts are automatically called from the webapp.

Can you accept this request to make this functioanlity available for other TranSMART users? If you have any questions or would like more information, please let me know.

Thanks,
Erwin